DTU - Metagenomics applied to surveillance of pathogens and antimicrobial resistance
- Offered byCoursera
Metagenomics applied to surveillance of pathogens and antimicrobial resistance at Coursera Overview
Duration | 15 hours |
Start from | Start Now |
Total fee | Free |
Mode of learning | Online |
Official Website | Explore Free Course |
Credential | Certificate |
Metagenomics applied to surveillance of pathogens and antimicrobial resistance at Coursera Highlights
- 67% started a new career after completing these courses.
- Earn a shareable certificate upon completion.
- Flexible deadlines according to your schedule.
Metagenomics applied to surveillance of pathogens and antimicrobial resistance at Coursera Course details
- The field of metagenomics and whole community sequencing is a promising area to unravel the content of microbial communities and their relationship to disease and antimicrobial resistance in the human population. Bioinformatic tools are extremely important for making sense out of metagenomics data, by estimating the presence of pathogens and antimicrobial resistance determinants in complex samples. Combined with relevant explanatory data, metagenomics is a powerful tool for surveillance.
- In this course, we teach about the potential of metagenomics for surveillance and give the learners an overview of the steps and considerations in a metagenomics study. After this course, the learners will know:
- - the difference between the concepts of metagenomics and other microbial genomics
- - the need to use controls in different steps of a metagenomics study
- - the advantages of metagenomics for the surveillance of antimicrobial resistance
- - how sampling design, sample size, sample material and sample handling influence the outcome of a metagenomics study
- - sample processing for bacterial and viral metagenomics
- - different sequencing platforms and their possibilities regarding metagenomics
- - the steps involved in a general metagenomics study, including quality control, mapping to different databases, and read count analysis
- - the principles behind various tools available for analysis of metagenomics data
- - how to interpret read classification results
- - the need for epidemiology in surveillance
- - the concept of global and integrated surveillance
- - the challenges for the use of metagenomics in surveillance
- - the potential of metagenomics for surveillance
Metagenomics applied to surveillance of pathogens and antimicrobial resistance at Coursera Curriculum
From sampling to sequencing
Welcome
Introduction to metagenomics
Considerations and controls for metagenomic/microbiome projects
Introduction to antimicrobial resistance
Sampling for surveillance
Sampling at farms and slaughterhouses
Sample storage
Isolation of DNA from complex samples
Sample processing for viral metagenomics
Sequencing platforms
Glossary
Get started !
Introduction to metagenomics
Considerations and controls for metagenomic/microbiome projects
Introduction to antimicrobial resistance
Sampling for surveillance
Sampling at farms and slaughterhouses
Sample storage
Isolation of DNA from complex samples
Notes on library preparation
Sequencing platforms
Assessment case-study - part 1
Assessment case study - part 2
Module 1 assessment - part 1
Module 1 assessment - part 2
FROM READS TO RESULTS
General introduction to bioinformatics analysis of metagenomics data
Overview of available metagenomic analysis tools
MGmapper
ResFinder database
Demo of metagenomic classification using KRAKEN
Real example of metagenomic analysis - lessons learned
General introduction to bioinformatics analysis of metagenomics data
Overview of available metagenomic analysis tools
MGmapper
MGmapper - Best mode vs Full mode
ResFinder database
Assessment case-study - part 3
Samples sheet
Report A - FastQC results
Report B - MGmapper results
Report C - KRAKEN results
Report D
Module 2 assessment
Interpretation of results and potential of metagenomics for surveillance
Analysis and visualization of read count data
Metagenomic assembly and binning: reconstructing genomes from reads
Application of metagenomics in surveillance - methods (part 1)
Application of metagenomics in surveillance - methods (part 2)
Application of metagenomics in surveillance - opportunities and challenges
Farewell
Virtual Machine setup
Analysis and visualization of read count data
Metagenomic assembly and binning: reconstructing genomes from reads
Application of metagenomics in surveillance - methods
Potential of metagenomics for surveillance
Challenges of metagenomics for surveillance
Assessment case-study - part 4
Report D
Epidemiology sheet and Report E
Introduction
Final quiz - section I - Sampling
Final quiz - section II - Quality control
Final quiz - section III - Bioinformatics analysis of metagenomics
Final quiz - section IV - Interpretation of metagenomics results
Final quiz - section V - Final quiz - section V - Analysis of metagenomics results in a surveillance context
Extra material for final assessment
Module 3 assessment
Final quiz - section I - Sampling
Final quiz - section II - Quality control
Final quiz - section III - Bioinformatics analysis of metagenomics
Final quiz - section IV - Interpretation of metagenomics results
Final quiz - section V - Analysis of metagenomics results in a surveillance context